Soil organic nitrogen rather than fertilizer drives dinitrogen losses in flooded rice systems

Rice production underpins food security but relies heavily on nitrogen (N) fertilization, much of which is lost as gaseous emissions. Dinitrogen (N₂) represents the largest N loss, yet its sources remain poorly constrained because biological dinitrogen (N₂) fluxes are difficult to quantify against the atmospheric background. Here, we apply an in situ ¹⁵N tracing–membrane inlet mass spectrometry (¹⁵N–MIMS) technique to simultaneously measure N₂, ammonia (NH₃), and nitrous oxide (N₂O) emissions and partition their soil- versus fertilizer-derived origins across the growing season in conventional japonica rice and hybrid rice. We find that soil organic N (SON) accounts for most N₂ emissions (72 to 75%), overturning the prevailing assumption that fertilizer dominates this loss pathway, which is independently confirmed by a 14-y fertilization experiment. In contrast, NH₃ originates mainly from fertilizer (71 to 77%) and N₂O derives from both sources in near-equal proportions. We identify a previously unrecognized “microbial N pump”, in which rapid microbial assimilation of fertilizer-derived ammonium (NH⁴⁺) induces stoichiometric imbalance and stimulates SON mineralization, mobilizing soil-derived NH⁴⁺ that ultimately fuels N₂ emissions, with depleted SON partially replenished through microbial N turnover. Neglecting SON contributions causes systematic overestimation of fertilizer-derived N₂ and NH₃ losses by ~35%. Hybrid rice increases yield by 59% and reduces yield-scaled gaseous N losses by 43% through enhanced fertilizer uptake and microbial N use efficiency. Together, these findings reveal an underappreciated pathway of fertilization-driven soil N losses, revise N budgets for flooded rice systems, and demonstrate that cultivar-informed management can simultaneously enhance rice productivity and environmental sustainability.